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Understanding the dynamics of microbial communities has gained much attention in recent years. Modern genomic technologies based on Next Generation Sequencing have opened a wide range of possibilities for microbial identification and diversity studies. BaseClear offers complete solutions to extract DNA from your samples and the means to determine the composition of bacteria, and also for Archaea and fungi in a broad range of sample, including water, faeces and bioreactor specimens. 

The technical approach for this kind of studies is usually based on PCR amplification followed by sequencing of housekeeping or functional genes (for instance 16S, 18S, 23S or ITS). The generated data is then compared to microbial sequencing databases. Data analysis is performed by our in-house developed tool: the BaseClear Genome Explorer. Advantages of microbial diversity analysis (also referred to as 'microbial profiling', '16S profiling' or '16S metagenomics') studies based on Next Generation sequencing compared to classical methods include:

  • Identify thousands of microorganisms in one analysis
  • Identification of non-cultivable microorganisms
  • Determine the relative abundance of microorganisms
  • Extremely fast for screening of complex ecosystems
  • Better understanding and control of the microbial flora

Microbial diversity analysis using Next Gen sequencing can be applied in a wide variety of studies. For instance in food processing, probiotics, water safety testing, microbiome analysis, biofilms, fermentation, soil research (e.g. Rhizobia) and environmental samples. 



BaseClear offers complete bioinformatics solutions for microbial profiling analysis. Standard solutions for microbial profiling include 16S and/or ITS amplicon analysis for taxonomic classification and relative frequencies. Our managers are happy to discuss the ideal workflow that best fits your needs and budget. Our main drive is to make sure that your research questions are answered!

A schematic overview of a 16S-amplicon based approach: Illumina MiSeq reads are merged into overlapping pseudo-reads and subsequently aligned against a 16S database. Taxonomic classification is performed using an in-house protocol. Extended advice on the project setup and in-depth downstream analysis are available.


Our bioinformatics department has developed two state-of-the-art microbial profiling analysis pipelines. The 16S based amplicon analysis protocol generally involves the Illumina MiSeq sequencing platform which is capable of producing paired-end reads of length 300 nt. Alternatively also the Illumina HiSeq and PacBio SMRT platforms can be used to generate shorter and longer reads, respectively. Depending on your research question and available budget, BaseClear can offer the best possible strategy that guarantees an optimal output. In most cases Illumina MiSeq paired-end reads are generated which are merged into overlapping pseudo-reads using our bioinformatics analysis pipeline. In this manner a relatively long stretch of the 16S rRNA gene can be covered (e.g. the V3-V4 region). Subsequently each read is aligned against a 16S rRNA gene database for taxonomic classification.

The standard output includes a comprehensive table containing all taxonomies found and their counts, but also a number of publication-ready figures which allow an easy (graphical) interpretation of the findings (e.g. a cladogram, pie chart and bar chart). The results can also be easily viewed and compared in an interactive manner using our unique online genome explorer.


Our 16S amplicon-based analysis protocol includes the generation of easy-to-interpret tables and figures. For example the Taxonomic pie chart displayed in the figure provides a clear overview of the taxonomic classifications and relative abundance. Alternatively taxonomic data can be easily (and interactively) explored with zoomable Krona pie chart (Ondov BD, Bergman NH, and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30; 12(1):385.). 

  • Taxonomy table containing a summary of all read-annotations and their relative abundance.
  • Publication-ready figures and plots (bar chart, pie chart, cladogram).
  • Microbial profiling analysis report containing a summary of the 16S annotation results.
  • Access to our Genome Explorer which allows interactive analyses of the results.



BaseClear is specialized in microbial diversity studies for environmental (e.g. food, water and soil) and microbiota samples. We offer complete solutions based on 16S (for bacteria) and/or ITS (for fungi) amplicon analysis for taxonomic classification and determine relative frequencies. Our managers are happy to discuss the ideal workflow that best fits your needs and budget. Our main drive is to make sure that your research questions are answered!


  • BaseClear has a strong focus on microbial genomics
  • Many years of experience with microbial profiling projects with samples coming from a variety of different source (e.g. soil, water, food products, feces, etc.) 
  • Experimental design for this kind of projects is crucial, our specialists can help decide which strategy should be used for your project for most reliable results
  • Advanced pipelines for downstream data analysis and interpretation
  • Taxonomic and functional classification performed using specialized software (such as MEGAN)
  • Unique interactive online portal for multilevel taxonomic analysis
  • BaseClear is an independent service laboratory using ISO17025 and GMP compliant methods 
  • Many satisfied customers worldwide

Meet Tom van den Bogert!

Tom is responsible for all metagenomics and microbial profiling projects, which are based on our next generation sequencing technologies, and the development of related approaches.

Testimonial DuPont Industrial Biosciences

The support that BaseClear has provided in the field of bioinformatics and downstream processing of next generation sequencing data has been extremely important for us. There are of course other organisations that offer next generation sequencing but that does not mean that you have everything you need. BaseClear's extra service is unique and represents one of their great strengths.

Senior Scientist


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